2020
Cytoskeletal Drugs Modulate Off-Target Protein Folding Landscapes Inside Cells
Davis CM, Gruebele M. Cytoskeletal Drugs Modulate Off-Target Protein Folding Landscapes Inside Cells. Biochemistry 2020, 59: 2650-2659. PMID: 32567840, DOI: 10.1021/acs.biochem.0c00299.Peer-Reviewed Original ResearchConceptsCytoskeletal drugsPhosphoglycerate kinaseActin filamentsDynamic cytoskeletal networksEffects of cytoskeletonProtein energy landscapesOff-target proteinsOpposite responseCytoskeletal networkProtein stabilityCellular milieuProtein-like sequencesVariable major protein-like sequenceOverall cell volumeCytoskeletonCell migrationEnergy landscapeMacromolecular crowdingMacromolecular crowdersProteinNonspecific surface interactionsTarget effectsMicrotubulesCytoplasmCellsAn in vitro mimic of in‐cell solvation for protein folding studies
Davis CM, Deutsch J, Gruebele M. An in vitro mimic of in‐cell solvation for protein folding studies. Protein Science 2020, 29: 1046-1054. PMID: 31994240, PMCID: PMC7096716, DOI: 10.1002/pro.3833.Peer-Reviewed Original ResearchConceptsPhosphoglycerate kinaseLysis bufferCytoplasmic protein interactionsSignificant nonadditive effectsVariety of proteinsProtein folding studiesEukaryotic cellsProtein foldingProtein interactionsCellular crowdingProtein-like sequencesEffect of FicollFolding studiesHydrophobic patchVariable major protein-like sequenceNonadditive effectsCellular effectsProteinCell environmentInert macromoleculesBiomolecular interactionsCellsTest tubeSmall crowdersMimics
2017
Binding, folding and insertion of a β-hairpin peptide at a lipid bilayer surface: Influence of electrostatics and lipid tail packing
Reid KA, Davis CM, Dyer RB, Kindt JT. Binding, folding and insertion of a β-hairpin peptide at a lipid bilayer surface: Influence of electrostatics and lipid tail packing. Biochimica Et Biophysica Acta (BBA) - Biomembranes 2017, 1860: 792-800. PMID: 29291379, PMCID: PMC5780206, DOI: 10.1016/j.bbamem.2017.12.019.Peer-Reviewed Original ResearchConceptsΒ-hairpin peptidesSVS-1POPC/POPG bilayersPOPC bilayersAtomistic molecular dynamics simulationsLipid bilayersInfluence of electrostaticsLipid bilayer surfaceMolecular dynamics simulationsCircular dichroism studiesCHARMM C36DPPG lipidsMixture of DPPCPOPG bilayersSpectroscopic studiesTail packingBilayer surfaceHydrophobic interactionsForce fieldHeadgroup packingTransient foldingDPPC bilayersDichroism studiesDynamics simulationsFluorescent peptidesParallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation
Zanetti‐Polzi L, Davis CM, Gruebele M, Dyer RB, Amadei A, Daidone I. Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation. FEBS Letters 2017, 591: 3265-3275. PMID: 28881468, PMCID: PMC5658256, DOI: 10.1002/1873-3468.12836.Peer-Reviewed Original ResearchAmino Acid MotifsKineticsModels, MolecularMolecular Dynamics SimulationNIMA-Interacting Peptidylprolyl IsomeraseProtein Conformation, alpha-HelicalProtein Conformation, beta-StrandProtein DomainsProtein EngineeringProtein FoldingProtein UnfoldingQuantum TheorySpectrophotometry, InfraredThermodynamics
2013
Dynamics of an Ultrafast Folding Subdomain in the Context of a Larger Protein Fold
Davis CM, Dyer RB. Dynamics of an Ultrafast Folding Subdomain in the Context of a Larger Protein Fold. Journal Of The American Chemical Society 2013, 135: 19260-19267. PMID: 24320936, PMCID: PMC3949483, DOI: 10.1021/ja409608r.Peer-Reviewed Original Research
2012
Raising the Speed Limit for β‑Hairpin Formation
Davis CM, Xiao S, Raleigh DP, Dyer RB. Raising the Speed Limit for β‑Hairpin Formation. Journal Of The American Chemical Society 2012, 134: 14476-14482. PMID: 22873643, PMCID: PMC3443077, DOI: 10.1021/ja3046734.Peer-Reviewed Original Research